res a/*/*/* | Leave only atoms which belong to chain A. |
res * exc m/*/*/ca | Leave only CA atoms which belong to chain M. |
res */*/*/* exc ca,c,n,o | Remove CA, C, N and O atoms from the selection. |
res a/* exc 72-112/*/ca | Leave only CA atoms which belong to chain A, but exclude residues 72-112. |
res 1-100 | Leave only atoms which belong to residues from 1 to 100. |
res 1-100 exc 20-40 | Leave only atoms which belong to residues 1-100, but exclude 20-40. |
res 1, 4, 8, 11-48 exc 20-32 |
Leave atoms which belong to residues 1, 4, 8, 11-48
but exclude residues 20-32. |
res phe,tyr,trp | Restrict selection to PHE, TYR and TRP. |
res ato 1-100 |
Restrict the current selection to atoms which have
serial numbers in the range between 1 and 100. |
res 1-20 40-50 |
Restrict the current selection to atoms which have
serial numbers between 1 and 20 and between 40 and 50. |
res *
res all |
Leave the selection unchanged (trivial, useless). |
res abo
res above |
Restrict to atoms above the plane. |
res aci
res acidic |
Leave only acidic amino-acids in the selection (GLU and ASP). |
res ali
res aliphatic |
Leave only aliphatic amino acids (ILE, LEU and VAL). |
res alt | Restrict to atoms at alternate positions. |
res bad |
Restrict selection to bad residues. A residue is treated as
bad if the peptide bond assigned to this residue is non-planar. The peptide bond is non-planar if the omega angle is different for 20 or more degrees from 0 or 180 degrees. |
res bas
res basic |
Leave only basic amino acids (ARG, LYS and HIS). |
res bel
res below |
Restrict to atoms below the plane. |
res cha
res charged |
Leave only charged amino acids (ARG, LYS, HIS, GLU and ASP). |
res cis | Restrict selection to cis residues. |
res com
res complement |
Leave only atoms which were not select previously. |
res het
res hetero |
Leave only hetero atoms (heme groups, water etc.). |
res pho
res hydrophobic |
Leave only hydrophobic amino acids
(ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS). |
res mai
res main_chain |
Leave only main chain atoms (CA, C, N and O). |
res mod serial_number
res model serial_number |
Restrict to a model specified by serial_number.
NMR structure is a set of models. Example: res mod 1 |
res pat
res pattern |
Restrict to the sequence pattern. The command
PAT (PATTERN) is used to define the sequence pattern. |
res neg
res negative |
Leave only negatively charged amino acids (GLU and ASP). |
res pol
res polar |
Leave only polar amino acids
(ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR). |
res seq
res sequence |
Restrict to sequence fragments which match the sequence
stored to the sequence buffer. The sequence buffer should be initialized before executing this command. |
res pos
res positive |
Leave only positively charged amino acids (ARG, LYS and HIS). |
res sid
res side_chains |
Leave only atoms which belong to side chains (all except CA, C, N and O). |
res sma
res small |
Leave only small amino acids
(GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN). |
res sph
res sphere |
Restrict to the atoms inside the sphere. Use the command
RAD (RADIUS) to set the sphere radius. |
res tin
res tiny |
Leave only tiny amino acids (GLY,ALA and SER). |
res tm |
Restrict to the transmembrane part
(useful for membrane proteins). |
res tra
res trans |
Restrict selection to trans residues. |
res tri
res triplet |
If there are three (or more) positively charged residues in a fragment
of up to five protein residues, restrict the current set of selected atoms to these three residues. Detailed explanation may found in the article: D. Juretic, L. Zoranic and D. Zucic, Basic charge clusters and predictions of membrane protein topology, Journal of Chemical Information and Computer Sciences 42, No. 3, 620-632 (2002). |
res 2c3 |
If there are two (or more) charged residues in a fragment of
three residues, restrict the selection choosing only these residues. |
res 2cz3 |
If there are two (or more) charged or zwitterionic residues in
a fragment of three residues, restrict the selection choosing only these residues. |
res 3c4
res3cz4 res 3c5 res 3cz5 res 4c5 res 4cz5 res 3c6 res 3cz6 res 4c6 res 4cz6 res 5c6 res 5cz6 res 4c7 res 4cz7 res 5c7 res 5cz7 res 5c9 res 5cz9 |
Analogous to res 2c3 and res 2cz3.
The same restriction criteria may be defined using patterns, but these short keywords are more practical. |
res 5p7 |
If there are five or more polar residues in a fragment of seven residues,
restrict the selection choosing only these residues. The following residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP. |
res 6p7 |
If there are six or more polar residues in a fragment of seven residues,
restrict the selection choosing only these residues. The following residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP. |